HEADER METAL BINDING PROTEIN 29-JAN-24 8VUK TITLE THE CRYSTAL STRUCTURE OF BRUCELLA ABORTUS FTRB AT 1.3 ANGSTROM TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: EFEO-TYPE CUPREDOXIN-LIKE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FTRB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUCELLA ABORTUS; SOURCE 3 ORGANISM_TAXID: 235; SOURCE 4 GENE: BABS19_II07770; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BRUCELLA ABORTUS, IRON TRANSPORT, FTRABCD, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ROY,B.L.GARCIA REVDAT 2 06-AUG-25 8VUK 1 JRNL REVDAT 1 22-JAN-25 8VUK 0 JRNL AUTH A.KERKAN,K.HART,D.W.MARTIN,J.PAJSKI,B.AIDOO,B.L.GARCIA, JRNL AUTH 2 S.ROY,S.DASGUPTA,S.HEMATIAN,A.SANTISTEBAN-VEIGA,N.J.SCHAAF, JRNL AUTH 3 S.BANERJEE JRNL TITL IN VITRO STRUCTURAL AND FUNCTIONAL STUDIES OF A NOVEL JRNL TITL 2 CUPREDOXIN, FTRB, FROM BRUCELLA ABORTUS 2308. JRNL REF ACS OMEGA V. 10 12653 2025 JRNL REFN ESSN 2470-1343 JRNL PMID 40191301 JRNL DOI 10.1021/ACSOMEGA.5C00690 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 17291 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1726 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.8900 - 2.9800 0.94 1293 141 0.1845 0.1910 REMARK 3 2 2.9700 - 2.3600 0.98 1350 150 0.1768 0.1862 REMARK 3 3 2.3600 - 2.0600 0.98 1328 145 0.1691 0.1828 REMARK 3 4 2.0600 - 1.8700 0.96 1332 147 0.1606 0.1934 REMARK 3 5 1.8700 - 1.7400 0.96 1328 145 0.1723 0.2199 REMARK 3 6 1.7400 - 1.6400 0.95 1307 139 0.1701 0.1593 REMARK 3 7 1.6400 - 1.5600 0.95 1284 154 0.1762 0.2007 REMARK 3 8 1.5600 - 1.4900 0.95 1287 141 0.1863 0.2168 REMARK 3 9 1.4900 - 1.4300 0.94 1282 151 0.1918 0.2385 REMARK 3 10 1.4300 - 1.3800 0.94 1303 148 0.2102 0.2628 REMARK 3 11 1.3800 - 1.3400 0.93 1273 130 0.2106 0.2437 REMARK 3 12 1.3400 - 1.3000 0.88 1198 135 0.2326 0.2602 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.375 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.016 728 REMARK 3 ANGLE : 1.445 989 REMARK 3 CHIRALITY : 0.111 111 REMARK 3 PLANARITY : 0.012 132 REMARK 3 DIHEDRAL : 14.096 281 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8VUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000281222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 28.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, PH 4.6, 20% V/V REMARK 280 PEG3350, SUPPLEMENTED WITH 20 MM MANGANESE CHLORIDE, 20 MM REMARK 280 COPPER(II) SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 TRP A 43 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 306 O HOH A 409 1.57 REMARK 500 O HOH A 303 O HOH A 392 1.87 REMARK 500 OE1 GLU A 113 O HOH A 301 1.90 REMARK 500 OD1 ASP A 55 O HOH A 302 1.93 REMARK 500 O HOH A 311 O HOH A 398 1.93 REMARK 500 O HOH A 354 O HOH A 389 2.06 REMARK 500 O HOH A 301 O HOH A 404 2.07 REMARK 500 O HOH A 355 O HOH A 389 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 393 O HOH A 402 1545 1.83 REMARK 500 O HOH A 367 O HOH A 382 1545 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 108 148.89 -176.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 429 DISTANCE = 6.88 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 84 OE1 REMARK 620 2 GLU A 86 OE1 84.5 REMARK 620 3 ASP A 119 OD2 96.9 85.7 REMARK 620 4 HOH A 304 O 93.8 93.5 169.1 REMARK 620 5 HOH A 339 O 95.9 175.5 89.8 90.9 REMARK 620 6 HOH A 363 O 170.5 87.6 87.8 81.3 92.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 OD1 REMARK 620 2 HOH A 319 O 86.5 REMARK 620 3 HOH A 334 O 100.2 75.5 REMARK 620 4 HOH A 343 O 89.8 94.0 164.9 REMARK 620 5 HOH A 370 O 85.9 167.5 96.1 95.9 REMARK 620 6 HOH A 406 O 169.5 94.1 90.1 79.7 95.2 REMARK 620 N 1 2 3 4 5 DBREF1 8VUK A 43 132 UNP A0A0F6AV93_BRUA1 DBREF2 8VUK A A0A0F6AV93 43 132 SEQRES 1 A 90 TRP ALA GLU GLU PRO THR PHE ARG LEU GLU PHE LYS ASP SEQRES 2 A 90 GLY VAL ILE THR PRO ASP ARG LEU GLU VAL PRO ALA ASN SEQRES 3 A 90 THR ARG PHE ARG ILE GLU LEU VAL ASN THR GLY SER MET SEQRES 4 A 90 PRO ALA GLU PHE GLU SER LEU GLU LEU ARG LYS GLU LYS SEQRES 5 A 90 VAL ILE ALA ALA GLN SER GLU THR VAL MET VAL ILE ARG SEQRES 6 A 90 THR LEU ASP PRO GLY GLU TYR PRO PHE PHE ASP ASP PHE SEQRES 7 A 90 HIS PRO GLY GLY THR PRO ALA ILE LEU ILE ALA LYS HET MN A 201 1 HET MN A 202 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN 2(MN 2+) FORMUL 4 HOH *129(H2 O) SHEET 1 AA1 4 VAL A 57 THR A 59 0 SHEET 2 AA1 4 THR A 48 LYS A 54 -1 N GLU A 52 O THR A 59 SHEET 3 AA1 4 PHE A 71 ASN A 77 1 O GLU A 74 N PHE A 49 SHEET 4 AA1 4 SER A 100 ILE A 106 -1 O THR A 102 N LEU A 75 SHEET 1 AA2 5 ARG A 62 PRO A 66 0 SHEET 2 AA2 5 ALA A 127 LYS A 132 1 O ILE A 130 N LEU A 63 SHEET 3 AA2 5 GLY A 112 ASP A 118 -1 N GLY A 112 O ALA A 131 SHEET 4 AA2 5 ALA A 83 SER A 87 -1 N GLU A 86 O PHE A 117 SHEET 5 AA2 5 LYS A 92 ILE A 96 -1 O ILE A 96 N ALA A 83 LINK OE1 GLU A 84 MN MN A 201 1555 1555 2.15 LINK OE1 GLU A 86 MN MN A 201 1555 1555 2.18 LINK OD2 ASP A 119 MN MN A 201 1555 1555 2.02 LINK OD1 ASP A 119 MN MN A 202 1555 1555 2.14 LINK MN MN A 201 O HOH A 304 1555 1555 2.12 LINK MN MN A 201 O HOH A 339 1555 1556 2.20 LINK MN MN A 201 O HOH A 363 1555 1555 2.16 LINK MN MN A 202 O HOH A 319 1555 1556 1.99 LINK MN MN A 202 O HOH A 334 1555 1556 2.23 LINK MN MN A 202 O HOH A 343 1555 1556 2.19 LINK MN MN A 202 O HOH A 370 1555 1555 2.21 LINK MN MN A 202 O HOH A 406 1555 1556 2.29 CISPEP 1 THR A 59 PRO A 60 0 -9.26 CRYST1 25.811 27.033 30.821 83.41 69.64 71.81 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.038743 -0.012731 -0.014290 0.00000 SCALE2 0.000000 0.038938 -0.000269 0.00000 SCALE3 0.000000 0.000000 0.034608 0.00000 CONECT 652 1420 CONECT 687 1420 CONECT 1220 1421 CONECT 1221 1420 CONECT 1420 652 687 1221 1425 CONECT 1420 1484 CONECT 1421 1220 1491 CONECT 1425 1420 CONECT 1484 1420 CONECT 1491 1421 MASTER 295 0 2 0 9 0 0 6 837 1 10 7 END